It depends on the time of day, the radar/forcast, etc.
They have a standard amount of time and distance things need to be cleared when lightening and thunder are present. If it is 4:00 in the afternoon and lightening strikes, they'll close. If it's 10:15 am, they'll delay, close to new arrivals, and reopen after the appropriate amount of time.
All of this being said, there aren't many "inside" places at the water parks, and you really should t be outside when there is lightening. I suppose that decision is up to you. Of course, if you rode a Disney bus to get there, you may be outside for a while anyway waiting for the park to clear. In my experience, it's the least efficient bus loop in the World.